Managing Your Notebooks

Managing Your Notebooks

Installing Python Packages

You can install additional Python packages as needed:

# In a notebook cell:
!pip install pandas scikit-learn seaborn

# Or for bioinformatics packages:
!pip install biopython pysam

Installed packages persist between sessions, so you only need to install them once.

Organizing Your Work

Best practices for notebook organization:

• Create descriptive notebook names (e.g., rnaseq_quality_analysis_2024.ipynb)
• Use folders within notebooks/ to organize projects
• Document your analysis with markdown cells
• Save notebooks regularly (Ctrl+S or Cmd+S)

Data Persistence

• Everything in the notebooks/ folder persists between sessions
• Installed Python packages are preserved
• Kernel state is not preserved - variables need to be recomputed when reopening notebooks